BioChem Module 2

What are the four components of an α-amino acid?

An α carbon linked to an amino group, a carboxylic acid group, a hydrogen atom, and a distinctive R group (side chain).

At neutral pH, what charge does the amino group of an amino acid carry?

Positively charged.

At neutral pH, what charge does the carboxyl group of an amino acid carry?

Negatively charged.

What is a zwitterion?

A dipolar ion; at neutral pH, a free amino acid exists with a charged amino group (NH3+) and carboxyl group (COO−).

What are the two possible stereoisomers of amino acids?

The D isomer and the L isomer.

Which isomer of amino acids is found in proteins?

The L isomer.

Into what four groups can the 20 amino acids be placed?

Hydrophobic, polar, positively charged, and negatively charged.

Which amino acid is the simplest and achiral?

Glycine.

Which amino acid is the bulkiest hydrophobic amino acid?

Tryptophan.

What side chain group does cysteine contain?

A sulfhydryl (thiol, –SH) group.

What can pairs of cysteine –SH groups form?

Disulfide bonds, which are important in protein stabilization.

Why is histidine often found in enzyme active sites?

Its imidazole ring can bind and release protons during enzymatic reactions.

What is histidine's approximate pKa value?

Near 6, close to physiological pH.

What functional group does arginine contain?

A guanidinium group.

What are aspartic acid and glutamic acid commonly called in their deprotonated forms?

Aspartate and glutamate.

What is the typical pKa of the terminal α-carboxyl group?

3.1

What is the typical pKa of aspartic/glutamic acid side chains?

4.1

What is the typical pKa of histidine's side chain?

6.0

What is the typical pKa of the terminal α-amino group?

8.0

What is the typical pKa of cysteine's side chain?

8.3

What is the typical pKa of tyrosine's side chain?

10.0

What is the typical pKa of lysine's side chain?

10.4

What is the typical pKa of arginine's side chain?

12.5

What is a peptide (amide) bond formation reaction?

Linking the α-carboxyl group of one amino acid to the α-amino group of another, with loss of a water molecule.

What is a "residue" in a polypeptide chain?

Each amino acid unit in the chain.

Which end of a polypeptide chain is at the beginning by convention?

The α-amino group (N-terminus).

What is the mean molecular mass of an amino acid?

110 g/mol.

What is 1 dalton equal to?

1 atomic mass unit.

What is cystine?

Two cysteine residues linked by a disulfide bond.

Who determined the amino acid sequence of insulin, and when?

Frederick Sanger, in 1953.

Why is the peptide bond essentially planar?

Because of resonance, giving it partial double-bond character and prohibiting rotation.

What is the C–N distance in a peptide bond?

1.32 Å (between a single bond's 1.49 Å and a double bond's 1.27 Å).

Which configuration of the peptide bond is usually favored, trans or cis?

Trans.

Why is the trans configuration favored over cis?

Steric repulsion between groups attached to the α-carbon atoms hinders the cis configuration.

Which amino acid can adopt both cis and trans configurations relatively easily?

Proline.

What are torsion (dihedral) angles phi (φ) and psi (ψ)?

Rotation about the N–Cα bond (φ) and the Cα–carbonyl carbon bond (ψ).

What does a Ramachandran plot show?

The φ and ψ angles that are sterically allowed for a polypeptide.

What fraction of possible (φ, ψ) combinations are excluded by steric clashes?

About three-quarters.

What is secondary structure?

Three-dimensional structure formed by hydrogen bonds between backbone N–H and C=O groups of nearby residues.

What is primary protein structure?

The linear order of amino acid residues in a polypeptide chain.

What is tertiary protein structure?

The overall three-dimensional shape of a single polypeptide.

What is quaternary protein structure?

The arrangement of multiple polypeptide subunits in a multimeric protein complex.

In an α helix, which groups hydrogen bond to each other?

The C=O group of one residue bonds to the N–H group of the residue four positions ahead.

How many amino acid residues are in each turn of an α helix?

3.6 residues per turn.

What is the "pitch" of an α helix?

The length of one complete turn, equal to rise (1.5 Å) × residues per turn (3.6) = 5.4 Å.

What is the rise per residue along the α helix axis?

1.5 Å.

What handedness do nearly all α helices in proteins have?

Right-handed.

Why are right-handed α helices energetically favored?

They have less steric clash between side chains and the backbone.

Which amino acids tend to destabilize α helices due to β-carbon branching?

Valine, threonine, and isoleucine.

Which amino acids disrupt α helices by competing for main-chain H-bonds?

Serine, aspartate, and asparagine.

Why does proline disrupt α helices?

It lacks an NH group and its ring structure prevents the needed φ angle.

Why is proline called a "helix breaker"?

Its unusual R group creates a bend incompatible with helix formation.

What is a β strand?

A common form of secondary structure in which the polypeptide is almost fully extended.

What is the distance between adjacent amino acids along a β strand?

About 3.5 Å.

What are the three possible arrangements of strands in a β sheet?

Parallel, antiparallel, or mixed.

In a parallel β sheet, how do adjacent strands run?

In the same direction (N- and C-termini align).

In an antiparallel β sheet, how do adjacent strands run?

In opposite directions (N-terminus of one aligns with C-terminus of the other).

Which amino acids are often found in β-pleated sheets?

The aromatic amino acids: tryptophan, tyrosine, and phenylalanine.

What is a reverse turn (β turn)?

A structure allowing polypeptide chains to reverse direction, often with the CO of residue i hydrogen bonded to the NH of residue i+3.

What interactions primarily drive tertiary protein structure?

Interactions between R groups, including hydrogen bonding, ionic bonding, dipole-dipole interactions, van der Waals forces, and hydrophobic interactions.

Where do hydrophobic amino acids typically cluster in a folded globular protein?

On the inside of the protein.

What class of proteins is characterized by long, narrow strands and structural roles?

Fibrous proteins.

What class of proteins is characterized by compact, rounded shapes and functional roles?

Globular proteins.

Give two examples of fibrous proteins.

Collagen and myosin (also fibrin, elastin, keratin).

Give two examples of globular proteins.

Enzymes and hemoglobin (also insulin, immunoglobulin).

How does the amino acid sequence of fibrous proteins typically compare to globular proteins?

Fibrous proteins have repetitive sequences; globular proteins have irregular sequences.

How does solubility typically differ between fibrous and globular proteins?

Fibrous proteins are generally insoluble in water; globular proteins are generally soluble in water.

What is the quaternary structure of hemoglobin?

A heterotetramer composed of two α and two β subunits (α2β2).

What group is tightly associated with each hemoglobin subunit?

A heme group bound to iron.

How many oxygen molecules can a hemoglobin tetramer bind?

Four (one per subunit), binding cooperatively.

How does hemoglobin's oxygen-binding curve compare to myoglobin's?

Hemoglobin's is sigmoidal (cooperative); myoglobin's is hyperbolic.

What is myoglobin, and where is it found?

A heme-containing, monomeric oxygen-binding protein found in muscle tissue.

What is protein folding?

The spontaneous process by which a protein achieves its proper tertiary or quaternary conformation.

What forces primarily guide protein folding?

Hydrophobic interactions, hydrogen bonds, ionic bonds, and van der Waals forces.

What are chaperones?

A class of proteins that assist other proteins in folding correctly.

What is protein denaturation?

The loss of a protein's 3D structure, reverting it to an unstructured chain of amino acids.

Name two agents that can denature proteins.

Heat and high concentrations of urea or guanidine HCl.

What experiment demonstrated that primary structure determines 3D protein structure?

Christian Anfinsen's ribonuclease renaturation experiment.

What two reagents did Anfinsen use to denature ribonuclease?

Urea and β-mercaptoethanol.

What does urea do to a protein's structure?

Disrupts noncovalent bonds.

What does β-mercaptoethanol do to a protein's structure?

Fully reduces disulfide bonds.

How did Anfinsen restore ribonuclease's native structure?

By slowly removing urea and β-mercaptoethanol through dialysis.

What conclusion did Anfinsen's experiment support?

The information for a protein's 3D fold is inherent in its primary structure.

What conditions are needed to reestablish correct disulfide pairing in ribonuclease?

Urea must be removed, and a trace of β-mercaptoethanol must remain present.

Is protein folding a random search process?

No, it occurs by progressive stabilization of intermediates (cumulative selection), not random search.

What is "cumulative selection" in the context of protein folding?

A process where partly correct folding intermediates are retained because they are slightly more stable than unfolded regions.

What model describes protein folding via intermediate stabilization?

The nucleation-condensation model.

What does the "folding funnel" represent?

The thermodynamics of protein folding, from maximum entropy/minimal structure at the top to the folded protein at the bottom.

How much of secondary structure can be predicted from local sequence alone?

Only about 60–70%.

What are the two main approaches for predicting 3D structure from sequence?

Ab initio prediction and knowledge-based methods.

What type of protein aggregates are associated with Alzheimer, Parkinson, and Huntington disease?

Amyloid fibrils or plaques, rich in β sheets.

What are posttranslational modifications?

Alterations to a protein's structure that occur after its synthesis in the cell.

What deficiency prevents hydroxylation of collagen?

Lack of vitamin C.

What is a protein motif (supersecondary structure)?

A common combination of secondary structural elements, often associated with specific functions.

What motif is common in DNA-binding proteins?

The helix-turn-helix motif.

What is a protein domain?

An independently folding region within a polypeptide, often connected by a flexible linker.

What structural feature characterizes α-keratin?

Two right-handed α helices intertwined into a left-handed super helix (coiled coil).

What stabilizes the two helices of an α-keratin coiled coil?

Ionic and van der Waals interactions.

What is a heptad repeat in coiled-coil proteins?

An imperfect repeating sequence of seven amino acids, with leucine at every seventh position.

What amino acid appears at every third residue in collagen?

Glycine.